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Introduction to Plant Pathology BIOL 5408 Instructor: Erin Schuenzel Email: [email protected] – preferred contact method Office: Science 1.332 Office Phone: 956-381-2229 Office Hours: M 10-11, T 8-9, W 10-11 Course Description The aim of this course is to familiarize the student with a general introduction to plant pathology. Students will be introduced to the major viral, bacterial and fungal pathogens with focus on those found in the Lower Rio Grande Valley. Students will also understand how plants can respond to the microbes on a cellular and organismal level. The disease triangle and current means of molecular identification will be explored in the lab. Texts Essential Plant Pathology 2nd Ed. (2009) by G.L. Schumann and C.J. D’Arcy, APS Press ISBN 978-0-89054318-8 – Required Plant Pathology 5th Ed. (2005) by G. N. Agrios, Academic Press, Inc. – Required (will be provided) Course Requirements Presentations: All powerpoint presentations will be available before class in the Content folder on the class Blackboard site. Lecture Quizzes: All quizzes will involve two-parts, an individual portion and a group portion. The individual portion of the quiz will take in the first 15 minutes of class. The second part of the quiz is to answer the same five questions as a group within a 10 minute time period. Each quiz will have five multiple-choice questions. The individual portion is 10 points and the group portion is 30 points for a total quiz grade of 20 points. Your nine highest quiz grades will be used for the final grade. Because this is a group quiz – NO MAKE-UPS POSSIBLE. All quizzes are scheduled in advanced. Topics are listed below in the calendar portion of the syllabus. There are eight quizzes, your seven highest are kept for grading. Term Paper: Each student will choose a plant disease to explore that is affecting or could affect plants in the Rio Grande Valley. This paper will essentially be a literature review on the pathogen. The paper is expected to include general information on the pathogen (taxonomy, economic impact), how the disease spreads, the infection process, how the disease is diagnosed and what control methods are currently being employed. The paper is due the last day of class, May 2nd, at 11pm through blackboard. The term paper will be graded for content, clarity, accuracy and grammar. Outside Essay Exams: The two exam essays will be posted on-line throughout the semester and will be turned in through the classroom management system. Students will have a week (7 days) to turn-in their essay. An official rubric for grading will be posting with the essay. In general, these essays cover broad topics and should typically run 3-5 typed pages. All essays will be graded for content, clarity, accuracy and grammar. Laboratory: Each student must be enrolled in an appropriate laboratory section. The laboratory grade will count for 35% of the final grade. The laboratory syllabus will be available on Blackboard. Group Work: At the beginning of the semester, you will form groups. These groups will be used for the group portion of the quizzes and group work done during class. Class Policies Grading Scale: Grade A B C D F Percentage x 90.0 89.9 x 80.0 79.9 x 70.0 69.9 x 60.0 59.9 x Point Totals: Quizzes (8 Lecture & 6 Lab) Outside Essay Exams Lab Reports Lab Notebooks Participation Term Paper (Graduate) 30% 20% 10% 16% 10% 14% (7 @ 30 points and 6 @ 15 points or 300 points) (2 @ 100 points each or 200 points) (2 @ 50 points each or 100 points) (1 @ 16% each or 160 points) (100 pints) (1 @ 14% or 140 points) Re-grades The focus of the class is to learn the material; not force you to remember all the facts in a timed format. Each outside essay exam and lab report, except the final lab report, can be turned in again to earn up to 10% of the points (for example full credit on the re-grade can result in a grade change from 65% to 75%). You cannot earn more points than possible for the quiz or exam (for example you score a 29/30 on a quiz, the highest you can earn is a 30/30 despite 2 points being available). The re-grade must be turned by Friday May 6th by 11pm to be considered. Late Essay Exams and Reports Late essay exams and reports will be penalized 10% each day for 5 days. After 5 days the exam or report will earn a 0. Students with Disabilities If you have a documented disability (physical, psychological, learning, or other disability which affects your academic performance) and would like to receive academic accommodations, please inform your instructor and contact Student Accessibility Services to schedule an appointment to initiate services. It is recommended that you schedule an appointment with Student Accessibility Services before classes start. However, accommodations can be provided at any time. Brownsville Campus: Student Accessibility Services is located in Cortez Hall Room 129 and can be contacted by phone at (956) 8827374 (Voice) or via email at [email protected]. Edinburg Campus: Student Accessibility Services is located in 108 University Center and can be contacted by phone at (956) 665-7005 (Voice), (956) 6653840 (Fax), or via email at [email protected]. Mandatory Course Evaluation Period Students are required to complete an ONLINE evaluation of this course, accessed through your UTRGV account (http://my.utrgv.edu); you will be contacted through email with further instructions. Online evaluations will be available when notified. Students who complete their evaluations will have priority access to their grades. Attendance Students are expected to attend all scheduled classes and may be dropped from the course for excessive absences. UTRGV’s attendance policy excuses students from attending class if they are participating in officially sponsored university activities, such as athletics; for observance of religious holy days; or for military service. Students should contact the instructor in advance of the excused absence and arrange to make up missed work or examinations. Scholastic Integrity As members of a community dedicated to Honesty, Integrity and Respect, students are reminded that those who engage in scholastic dishonesty are subject to disciplinary penalties, including the possibility of failure in the course and expulsion from the University. Scholastic dishonesty includes but is not limited to: cheating, plagiarism, and collusion; submission for credit of any work or materials that are attributable in whole or in part to another person; taking an examination for another person; any act designed to give unfair advantage to a student; or the attempt to commit such acts. Since scholastic dishonesty harms the individual, all students and the integrity of the University, policies on scholastic dishonesty will be strictly enforced (Board of Regents Rules and Regulations and UTRGV Academic Integrity Guidelines). All scholastic dishonesty incidents will be reported to the Dean of Students. Sexual Harassment, Discrimination and Violence In accordance with UT System regulations, your instructor is a “responsible employee” for reporting purposes under Title IX regulations and so must report any instance, occurring during a student’s time in college, of sexual assault, stalking, dating violence, domestic violence, or sexual harassment about which she/he becomes aware during this course through writing, discussion, or personal disclosure. More information can be found at www.utrgv.edu/equity, including confidential resources available on campus. The faculty and staff of UTRGV actively strive to provide a learning, working, and living environment that promotes personal integrity, civility, and mutual respect in an environment free from sexual misconduct and discrimination. Course Drops According to UTRGV policy, students may drop any class without penalty earning a grade of DR until the official drop date. Following that date, students must be assigned a letter grade and can no longer drop the class. Students considering dropping the class should be aware of the “3-peat rule” and the “6-drop” rule so they can recognize how dropped classes may affect their academic success. The 6-drop rule refers to Texas law that dictates that undergraduate students may not drop more than six courses during their undergraduate career. Courses dropped at other Texas public higher education institutions will count toward the six-course drop limit. The 3-peat rule refers to additional fees charged to students who take the same class for the third time. Week Date Subject Readings Quiz/Essay Week 1 Jan-21 Introduction to Plant Pathology Plant Taxonomy, Plant Morphology & Physiology Schumann & D’Arcy Ch. 1 On BB Learn On BB Learn Week 2 Jan-28 Plant Morphology & Physiology Plant Immunology General Microbiology On BB Learn On BB Learn Quiz 1 Week 3 Feb-4 Viruses Bacteria S & A Ch. 5; Agrios – pages 724-733 S & A Ch. 3; Agrios – pages 618-626, 687-691 Quiz 2 Week 4 Feb-11 Fungi Bacteria & Viruses S & A Ch. 2; Agrios – pages 386-404 Undergraduate Student Presentations Week 5 Feb-18 Oomycetes Other Eukaryotes Fungi Agrios – pages 404-432 S & A Ch. 4 & 6; Agrios – pages 705-719, 826-835 Undergraduate Student Presentations Week 6 Feb-25 Abiotic Factors Plant Disease and Disease Cycles Eukaryotes S & A Ch. 7; Agrios – pages 251-262, 358-383 S& A Ch. 8; Agrios – pages 77-102 Undergraduate Student Presentations Week 7 Mar-3 Epidemiology Disease Cycles S & A Ch. 10 & 11; Agrios – pages 266-273 Undergraduate Student Presentations Quiz 3 Week 8 Mar-10 Ecological Interactions Physiological Interaction S & A Ch. 9A S & A Ch. 9B Essay 1 Assigned Week 9 Mar-17 SPRING BREAK Week 10 Mar-24 Pathogen Genetics S & A Ch. 9C; Agrios – pages 125-165 Quiz 4 Week 11 Mar-31 Host Genetics S & A Ch. 9C; Agrios – pages 125-165 Quiz 5 Week 12 Apr-7 Pathogenicity Agrios – pages 139-165 Quiz 6 Week 13 Apr-14 Plant Response: Disease Agrios – pages 177-203 Week 14 Apr-21 Plant Response: Resistance Agrios – pages 208-246 Week 15 Apr-28 Graduate Presentations Term Paper Due SCHEDULE SUBJECT TO CHANGE Essay 1 Due Quiz 7, Essay 2 Assigned Essay 2 Due Lab Schedule Jan-21 Microscopy (Fungi & Bacteria) Jan-28 Media Preparation Feb-4 Serial Dilution, Field Trip Feb-11 Immunoassay Diagnostics (Viruses) Quiz 2 – ELISA & CTV Feb-18 PCR and Sequence based Diagnostics (Bacteria) Quiz 3 – PCR, MLST, PSA, HLB Feb-25 RT-PCR based Diagnostics (Bacteria) Quiz 4 – RT-PCR & HLB Mar-3 Next Generation Sequencing Quiz 5 - Sequencing Mar-10 Sequence Analysis, Pathogenicity Test Quiz 6 – Pathogenicity & PST Mar-17 SPRING BREAK Mar-24 Pathogenicity Test Mar-31 Pathogenicity Test Apr-7 Unknown Pathogen Apr-14 Unknown Pathogen Apr-21 Unknown Pathogen Apr-28 Graduate Student Presentations May-5 Lab Notebook Due May-9 Lab Report – Unknown Pathogen Due Quiz 1 – Media & Microscopy Lab Report – Pathogenicity Due